pathway analysis tools

Question

[siyu]

Does anyone know any tools that can analyze a broken gene's influence on the KEGG pathway?

thanks~!

Answer 1

[nilakshafreezon]

Have you looked at KEGGscape ?

[siyu]

thanks! If I know a gene which is destroy by a stop-codon mutation, I want to know its influence on corresponding pathway. Can the KEGGscape implement it ?

[nilakshafreezon]

I hope so, Im not quite sure though. That's why I gave it as an option so you could check out for your self.

Answer 2

[pld]

I'm not sure that any pathway enrichment programs can make that analysis for you. Correct me if I'm wrong, but I don't think Cytoscape/KEGGscape has any sort of simulation capabilities, they're more for annotation/curation/visualization. Your task falls more under topology analysis and other classes modeling approaches.

It looks like someone has a Cytoscape plugin

http://www.cbmc.it/~scardonig/interference/Interference.php

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088938

You could build your pathway up using KEGG and then push this data into the plugin above. That seems like a reasonable approach.

Lastly, you could poke away at it manually, maybe look at the immediate downstream nodes your protein interacts with and try and see if you can understand what happens when your protein fails to exert whatever interactions on these. You could also poke around in pubmed to see if someone has run the wet work on either a knockout of your protein, or mutations to downstream proteins mimicking whatever effects a knockout of your protein would have.

Or see if someone has a kinetic/etc model of the pathway you're interested in and set the concentration of your protein of interest to zero. COPASI is pretty easy to play with once you learn it and someone else has the model already published.

[siyu]

thanks for your help! Cytoscape looks like a software, so I need to do it by hand one by one if I have mangs genes and some KEGG pathways. how can I write a script to work parallelly ?

Answer 3

[siyu]

thanks! If I know a gene which is destroy by a stop-codon mutation, I want to know its influence on corresponding pathway. Can the KEGGscape implement it ?